I wonder if ''Little Big Man'' was the first major movie to portray Custer in a negative way?

It seems like this era (1970) was a time when there started to be a more sophisticated view of the struggle between Native Americans and U.S. expansion.

This was also during a period when the military had become very unpopular with some due to the Vietnam War.

You might be right about the movie Little Big Man.
It's interesting that you brought this up because I recently watched the movie Posse filmed in 1975 and I was curious about the location of where it was filmed, but while reading online I discovered that Kirk Douglas who is very liberal produced, directed and starred in the movie and by design was aimed at the corruption of some politicians.

Kirk the marshal who wants to further his career to become a senator takes his posse and murders the bad guys rather than arrest them.

When the last bad guy [Bruce Dern] turns the table on Kirk, Kirk is willing to steal all the money the town has in order to save his own skin. In the end Kirks own posse turns on him as well as the town folk.

Another movie that caused a stir in politics [mainly senators] was "Mr. Smith goes to Washington" in 1939 starring Jimmy Stewart. I don't know if that movie was politically aimed but many politicians took it that way.